EVA: Neo Genesis
by Victorsaurus04
Summary: My slightly different take on the Rebuild Story.
1. Chapter 1

**ENTRY 1**

"Father, stop! Damn you! Why are you doing this?" Shinji's horrified screams echoed through the control room. The NERV command team watched as EVA unit 01 shut down, limp and battered against the side of the mountain. Shinji had refused to engage the possessed EVA unit 03 containing Asuka, so the Dummy Plug System would be loaded and the EVA would be forced to fight. Although NERV had possibly lost one pilot inside the roaring monstrosity charging across the valley, an Angel was an Angel, and everyone knew what must done.

The inside of unit 01's plug lit with a menacing red light, and the visual surfaces were transformed into a hexagonal pattern showing countless streams of code and data through which Shinji could barely see. As he watched unit 03 charging at him, long tendrils emerged from the back of his seat and trapped his hands and wrists against the control handles. A long arm reached over him, blocking his view with a mechanical head containing a dozen alien-like red eyes that shifted and blinked spastically, appraising the dark form now leaping towards it. _My God, this is it_ , Shinji thought, _I am going to kill Asuka. I will have her blood on my hands and I'm powerless to stop it._

The force of the 9th Angel landing on unit 01 sent a shock wave across the valley. It grabbed unit 01's throat and began choking it. Inside the entry plug Shinji struggled to breathe, all the while cursing his father and the mechanical abomination that was about to take his friend's life. With a sickening crunch and rip, the Angel grew two new arms from its back. Freakishly long and ending in malformed clawed hands, they began to pummel and tear at unit 01. In the control room, warnings began to explode across the holo screen. Eva unit 01 was one hell of a machine, but it couldn't take this kind of beating for long. _Not yet, anyway_ thought Gendo.

"Damn it! How much longer until the Dummy System is active?" yelled Misato. Maya Ibuki was frantically shifting through information on her control station. "It's almost ready! 97…98…99… Active! The Dummy Plug System is online." "Unit 01 is at 78% armour capacity. Whatever this system is going to do it had better do it now!" added Aoba. A new window displayed on the holo screen showing the view from the Dummy System's perspective. The deranged face of unit 03 is all it saw as unit 01's head was hit again and again. They watched as unit 01 began to twitch and finally roar as it once again prepared for battle. It reached a hand up to hold off one of unit 03's clawed arms and another to grab it by the neck. Then just as suddenly as it had sprung to life, unit 01 shut down again.

The command team watched in shock as unit 03 was momentarily taken by surprise then began to rip at unit 01 again. "No, this shouldn't be happening! The synthetic harmonic duality program had been designed and calibrated using unit 01. Try to restart it, now!" barked Dr. Akagi. "We're trying ma'am," replied Hyuga "but the system isn't responding!" Above the commotion of the command team's panic, Gendo and Fuyutsuki watched stoically. The old professor leaned over to Gendo. "Unless you plan on destroying the only means you have of reuniting with her, I suggest taking a more drastic action," he whispered, agitated. Gendo remained unmoved as ever, even as Misato and the others began looking to him for instructions. Though he calmly told them to keep trying to the restart the system, Gendo was becoming worried. Angels are beings of unimaginable power, but ultimately only an EVA can kill another EVA. What had the Americans created with unit 03, and why? _Yui, my love… If you can hear me now, I need your help._

Maya gasped in shock. "The Magi are tracking another signal! Its twenty kilometers away from the battle at an altitude of fifty three thousand feet, and descending rapidly." As Hyuga kept fighting a losing battle with the Dummy System, Aoba turned his attention to the new object. "The Magi are trying to track its descent trajectory. We can't get a clear reading on its aural signature so the Magi can't determine if it's an Angel. Calculations will be complete in thirty seconds." As if on the same thought stream, Ritsuko, Misato, Gendo, and Fuyutsuki began remembering data gathered fifteen years ago during the Second Impact. Although the appearance of two or more Angels at the same time was theorized, it had never been proven. Only Dr. Katsuragi knew the answer, and it died with him when the first Angel Adam reached the point of singularity and destroyed half the world.

Aoba spoke "Point of impact should be eighteen kilometers from the battle. Wait, course is changing… It's headed towards Units 01 and 03 on a fast decent path. My God, it's not an Angel! It's…" "An Eva?!" shouted Misato. A collective gasp emerged from the command team and the dozens of support personnel inside headquarters. "Getting a visual now from long range observation cameras," said Maya. On the holo screen a live feed appeared of a blurry humanoid shape as it descended through the clouds. They could just make out the silvery white colour, with highlights and marks of red and black. It was descending head-first, two glowing blue eyes lighting the way. And on its back white wings somewhat folded back to guide it quickly and smoothly to its target like a bird of prey. _Wings? The Adam's Vessel prototype peripheral system… Could it be?_ thought Dr. Akagi. Deep in the bowels of NERV, Kaji monitored the situation with two laptops hooked up to the fiber optic lines leading to the Magi and headquarters. _Well then,_ _WILLE couldn't destroy you after all, unit 04._

The first transmissions were garbled at first, but as the Magi completed its calculations it zeroed-in on the frequency of this new target. "Come in Groom Lake actual. This is pilot Liam Alexander with EVA unit 04. Do you copy, over?" The pilot repeated his call twice more, but no one dared reply. EVA unit 04 was thought to be destroyed days ago. Could this be a trick, somehow created by the Angel possessing unit 03? "Groom Lake? Damn it, NERV Command, please respond! I am on descent towards a massive energy signature, and I am over unfamiliar land formations." Gendo Ikari cleared his throat, jolting everyone back to reality. Shinji was still screaming, begging Misato to do something. Monitor readings showed unit 01's armour compromised to fifty two percent. The Dummy Plug System still struggled to reactivate, but all in vain. Blessings are few and far in between, and must be taken advantage of. "First Lieutenant Hyuga, connect me to unit 04, do it now." ordered Commander Ikari.

"Evangelion unit 04, pilot Liam Alexander, this is Commander Gendo Ikari of NERV Japan." "NERV Japan? What the hell? This can't be happening." said Liam in exasperation, "if you are who you say you are, transmit your authentication code." Gendo activated a small screen and key board and transmitted the code. In his hiding spot, Kaji became very serious and said aloud to himself "Could he be asking for the Avenging Fire codes? Is this why WILLE didn't destroy it? Was unit 03 meant to be the target? That must mean the pilot of unit 04 has been briefed on WILLE's plans, but how does Ikari know of the treaty?" For Kaji, certain plans had just become more complicated, which meant keeping his gun a little closer to himself at night.

"Authentication code received. Sir, what the hell is going on here? Where is Groom Lake and North America Command?" Liam asked as a holographic display now showed him Commander Ikari. "Pilot, there is no time to explain. You are headed towards two Evangelions engaged in combat. One of them has been possessed by the 9th Angel." replied Gendo. Misato turned to the three technicians. "Transmit the data to him, quickly. He's just 3 kilometers from the EVAs now." As the data streamed into unit 04's entry plug, the visual surfaces activated into a full suite of tactical information. In headquarters, on the pilot information display for unit 04, the command team saw the pilot's face darken as the data for the 9th Angel displayed. He uttered one word, "Nemesis."

Unit 04 landed a mile away from the other EVAs. He could see the side of the mountain stained red as unit 01 struggled to reactivate. The monstrous form of unit 03 crouched over it, its body becoming more chaotic as spikes and various mutations appeared on its body as a result of the angelic possession. As unit 04's wings folded into a small egg-shaped device on its back, the 9th Angel stopped its attack on unit 01 and turned to face the new threat. Liam could see that the entry plug in the Angel's back was trying to eject, which meant a pilot was inside. Gendo smiled behind his folded hands. "Evangelion unit 04, destroy that Angel." Unit 04 assumed a combat stance and inside its pilot seemed to take a new focus. Liam grinned, "Evangelion unit 04, engaging the target!" Unit 04's AT-field activated with a ripple of energy as the Evangelion charged its enemy.


	2. Chapter 2

**Entry 2**

From Commander Ikari's office, several pairs of eyes silently watched the computer screens focused on the interrogation taking place deep within NERV headquarters. A tall woman sat across a table from a young man whose wrists were held to the table by magnetic clamps. Her red jacket stood out authoritatively in the darkness, while the EVA pilot's white and black suit shone in the light from the single lamp hanging from the ceiling. The woman's hand reached to open one of several folders marked 'TOP SECRET', this one also marked 'MAJ12 EYES ONLY' above a graphic of the American flag.

"State your name." Misato said firmly.

"Liam Alexander."

"State your rank and branch of service."

"Captain, United States Air Force."

"What is your duty in the USAF?"

"I am the designated pilot of Evangelion unit 04."

"When you arrived on the battlefield, you referred to the 9th Angel as 'Nemesis.' What does that mean?" Liam looked mildly disgusted as he answered, "Branch 2 in Massachusetts tried to use DNA from Unit 04's Angel core to clone the Angel's mind, or something. Those morons thought that if they could program an EVA with it that we could use it as a training tool, but at Branch 1 we knew it was a bad idea." Misato though about this for a few quiet seconds. This pilot clearly had some level of clearance, clearly more than the other EVA pilots. Did he know as much as Mari, or know about WILLE?

"When contact was established you asked for Commander Ikari's authentication code. Was there a particular reason?" Misato asked. "Security protocol, obviously." They stared at each other for a tense moment. In the darkness of Commander Ikari's office Kaji looked uneasy, thankfully the two old men couldn't tell. The pilot may not know of the Avenging Fire protocol, though that was still up for debate. Ikari certainly knew, but did his knowledge extend all the way up to WILLE? The backup plan began in secret by Misato, Kaji, Ritsuko, and a select few international leaders could be in danger.

Misato stared intently at the pilot. "A final question, pilot. 72 hours ago, NERV Brand 1 in Groom Lake was destroyed as Evangelion unit 4 was activated. Yet, here you are. A pilot who shouldn't be alive, and in the hangar an Evangelion with a working S2 engine. What do you remember of the activation incident?" Liam looked at Misato in disbelief, his hands clenched and trembling. "They're dead? Everyone? But- ", "Pilot, focus. What happened during the activation?" Liam looked back at her blankly. "Everything was set up, ready to go for activation. We began the activation with unit 04 attached to the power umbilical, the S2 engine at 25% power. At 75% the umbilical was disconnected, and when the engine reached 100% the inside of the entry plug went dark. About a minute later I lost comms, then nothing. Just cold and darkness. I remember waking up as I was falling over the mountains before engaging the Angel. The rest," Liam flexed his hands under the magnetic restraints, "is history."

Ritsuko spoke from an earpiece in Misato's ear, "It's possible that the S2 engine created some sort of field to counteract the EVA's own collapsing AT Field. As the engine stabilized it must have reversed the collapse and harmonized with Unit 04's AT Field, but as to why it appeared here that will need some more research done by the Magi. I doubt you'll get anything more out of the pilot." Misato stood up and walked to the door. She glanced back at Liam, "You will be released shortly. And I'm sorry, about Branch 1."

In Commander Ikari's office, the lights came back on, illuminating Dr. Fuyutsuki, Gendo, Kaji, and Ritsuko. Gendo looked at Kaji, "Go to Bethany, retrieve the Key and bring it here. The appearance of Unit 04 is unexpected, but it presents a significant advantage. Fuyutsuki, walk with me. It's time to update SEELE. Their reaction will give us insight as to their intent."

After several silent minutes Misato walked into Commander Ikari's office. Frustrated, she looked at Kaji and Ritsuko. "It would seem as though we have one hell of a problem." Kaji smiled as he wrapped his arm around her, "Nothing we can't handle sweetheart. You know, if you're that stressed…" Misato brushed his arm off, she hated when he was sarcastic in these situations. Their whole plan might fall apart now. Ritsuko broke the tension "Well here's what we do know, or at least, can hypothesize. North America clearly had more intended for Unit 03 than to be some drone. Two EVAs powered by S2 engines would give them an unrivaled advantage, being able to easily dispatch even Unit 01. It is possible that Ikari knows about Avenging Fire, but that would mean he was working with someone in North America who possible knew about the creation of WILLE." "Yes," Misato replied "which really puts a solid halt to our plan to destroy the EVAs." Kaji, again unaffected by the brevity of their situation began to collect his things to leave. "No, it doesn't. The plan is still a go. I will go to Bethany. I'll rig the Third Angel's restraint systems so it escapes, Mari will defeat the Angel and destroy the base by detonating Unit 05." Kaji looked back at Misato as he walked out, "Don't worry so much, babe." Misato turned away, but Ritsuko smiled. "You know we may not have much time. Maybe you should-" "Ritsuko, stop. Its best this way."

On their way to the Okinawa Naval Launch Site, Dr. Fuyutsuki quietly said "Those three are in your office again, I'm sure." Gendo smiled, "Yes, I'm sure they are. The Avenging Fire protocol will no longer benefit either of us. However, this organization, WILLE, they must be stopped. Once I have the Key we must accelerate our plans to stop SEELE once and for all. Unit 01 will become God, my God, and I will see Yui again."


End file.
